Table S1. List of genes represented in Rice TF Primer Platform (Caldana et al., 2007). Complete list of 2508 TF genes, their primer sequences and their corresponding PCR efficiencies. Genes were presented with version 2.0 and version 5.0 RGAP genome annotations. Table S2. Transcription factor genes with and without annotations in version 5.0 and 7.0 of RGAP Pseudomolecule. Table S3. Expression profile of transcription factor genes in IR64 control and stress-treated plants upon submergence. Recorded Ct, R2, Efficiency and ÎCt values for all reactions. The list of used reference genes and their distribution on the plates is also given. Table S4. Expression profile of transcription factor genes in IR64-Sub1 control and stress-treated plants upon submergence. Worksheets record Ct, R2, Efficiency and ÎCt values for all reactions. The list of used reference genes and their distribution on the plates is also given. Table S5. Promoter sequences of SUB1A-1 and SUB1A-2. Table S6. Moderated t-tests results from LIMMA package for identifying differentially expressed genes. P-values were recorded and FDR corrections were also performed. Table S7. Details about the list of differentially expressed genes and their putative functions. (DOCX 29Â kb

Bernd Mueller-Roeber (52311)

Namrata Singh (1971532)

Niharika Sharma (565938)

Sigrid Heuer (799122)

Slobodan Ruzicic (76565)

Trang Dang (4745475)

Ute Baumann (53658)

Rice

Abstract Background Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. Results Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression. Conclusion This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance

Niharika Sharma

Trang Minh Dang

Namrata Singh

Slobodan Ruzicic

Bernd Mueller-Roeber

Ute Baumann

Sigrid Heuer

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Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown

Sharma, N.

Tang, T. M.

Singh, N.

Ruzicic, S.

Mueller-Roeber, B.

Baumann, U.

Heuer, S.

Rothamsted Repository

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